Consensus time

Working directory should contain root atlas Seurat object, which is available on GEO under record GSE152766:

Root_Atlas.rds (or get it by running through notebook 2, 3, 4, 5, 6, 7, 8 & 9)

Working directory must contain subdirectories,supp_data

supp_data/ should contain the file:

Ground_Tissue_Atlas.rds (get it by running through notebook 8)
Ground_Tissue_Atlas_latent_time.txt (get it by running through notebook 9)
Epidermis_LRC_Atlas.rds (get it by running through notebook 8)
Epidermis_LRC_Atlas_latent_time.txt (get it by running through notebook 9, need to change tissue/lineage)
Columella_Atlas.rds (get it by running through notebook 8)
Columella_Atlas_latent_time.rds (get it by running through notebook 9,  need to change tissue/lineage)
Stele_Atlas.rds (get it by running through notebook 8)
Stele_Atlas_latent_time.rds (get it by running through notebook 9,  need to change tissue/lineage)

1. Ground Tissue

2. Epidermis + LRC

3. Columella

4. Stele

5. Integrate consensus time

6. Transfer consensus time group to extracted tissue